I just thought I would give an update to my situation here. Since I am new to Mala, I thought I would try a fresh install. So I re-extracted the files to a new folder, and started from scratch adding one thing at a time. So far everything is working as it should.
The first time, I launched Mala, built the gamelist, and continued to configure all the options without saving the changes as I went. I had no way of really knowing what threw a wrench in the system. This time I am taking things one step at a time, making sure everything works as I go. I have added layouts, sounds, gamelists, plug-ins, all without a hitch.
At this point I am thinking my original problem had to do with the way I created my gamelist, although I am not sure I could reproduce what I did.
Anyway, I just wanted to post an update... so far so good! Carry on...